Package ubic.gemma.core.loader.expression.geo.model

Class GeoSeries

java.lang.Object
ubic.gemma.core.loader.expression.geo.model.GeoData
ubic.gemma.core.loader.expression.geo.model.GeoSeries
All Implemented Interfaces:
Serializable
public class GeoSeries extends GeoData
Represents a set of GEO samples that were submitted together. In many cases this corresponds to a full study, but for studies that used more than one type of microarray (e.g., A and B chips in Affy sets), there will be two series.
Author:
pavlidis
See Also:

  • Constructor Details

    • GeoSeries

      public GeoSeries()

  • Method Details

    • isSuperSeries

      public boolean isSuperSeries()

    • setIsSuperSeries

      public void setIsSuperSeries(boolean isSuperSeries)

    • isSubSeries

      public boolean isSubSeries()

    • setIsSubSeries

      public void setIsSubSeries(boolean isSubSeries)

    • addContributor

      public void addContributor(GeoContact contributor)

    • addDataSet

      public void addDataSet(GeoDataset dataset)

    • addSample

      public void addSample(GeoSample sample)

    • addSamples

      public void addSamples(Collection<GeoSample> s)
      Add a group of samples to this series.
      Parameters:
      s - samples

    • addSubSeries

      public void addSubSeries(String value)

    • addToKeyWords

      public void addToKeyWords(String keyword)

    • addToPubmedIds

      public void addToPubmedIds(String id)
      Parameters:
      id - in format "1239954" or "1239954,2194919", etc. The latter will be split into two.

    • addToSeriesTypes

      public void addToSeriesTypes(GeoSeriesType type)

    • addToSummaries

      public void addToSummaries(String text)
      Add a summary to the series.

    • addToVariables

      public void addToVariables(Integer number, GeoVariable variable)

    • addToSupplementaryFiles

      public void addToSupplementaryFiles(String supplementaryFile)

    • getValues

      public GeoValues getValues(Collection<GeoSample> s)
      Get a subset of the values. This is only used for 'splitting' a series.
      Parameters:
      s - Samples to include data from.
      Returns:
      geo values

    • keepSamples

      public void keepSamples(Collection<GeoSample> samplesToKeep)
      Only keep the given samples.

    • removeSamples

      public void removeSamples(Collection<GeoSample> samplesToSkip)
      Clean up samples we have decided are ineligible (i.e., non transcriptomic)
      Parameters:
      samplesToSkip - the samples to remove

    • getSeriesId

      public String getSeriesId()

    • getStatus

      public String getStatus()

    • getSubmissionDate

      public String getSubmissionDate()

    • getPlatformId

      public String getPlatformId()

    • getSamples

      public Collection<GeoSample> getSamples()

    • getSeriesTypes

      public Collection<GeoSeriesType> getSeriesTypes()

    • getSubSeries

      public Collection<String> getSubSeries()

    • getVariables

      public Map<Integer,GeoVariable> getVariables()

    • getContributors

      public Collection<GeoContact> getContributors()

    • getDataSets

      public Collection<GeoDataset> getDataSets()

    • getKeyWords

      public Collection<String> getKeyWords()

    • getLastUpdateDate

      public String getLastUpdateDate()

    • getOverallDesign

      public String getOverallDesign()

    • getPubmedIds

      public Collection<String> getPubmedIds()

    • getReplicates

      public Map<Integer,GeoReplication> getReplicates()

    • getSampleCorrespondence

      public GeoSampleCorrespondence getSampleCorrespondence()

    • getSummaries

      public List<String> getSummaries()

    • getSupplementaryFiles

      public Collection<String> getSupplementaryFiles()

    • getValues

      public GeoValues getValues()

    • getWebLinks

      public Collection<String> getWebLinks()

    • setSeriesId

      public void setSeriesId(String seriesId)

    • setStatus

      public void setStatus(String status)

    • setSubmissionDate

      public void setSubmissionDate(String submissionDate)

    • setPlatformId

      public void setPlatformId(String platformId)

    • setContributors

      public void setContributors(Collection<GeoContact> contributors)

    • setDataSets

      public void setDataSets(Collection<GeoDataset> dataSets)

    • setKeyWords

      public void setKeyWords(Collection<String> keyWords)

    • setLastUpdateDate

      public void setLastUpdateDate(String lastUpdateDate)

    • setOverallDesign

      public void setOverallDesign(String overallDesign)

    • setPubmedIds

      public void setPubmedIds(Collection<String> pubmedIds)

    • setReplicates

      public void setReplicates(Map<Integer,GeoReplication> replicates)

    • setSampleCorrespondence

      public void setSampleCorrespondence(GeoSampleCorrespondence sampleCorrespondence)

    • setSummaries

      public void setSummaries(List<String> summaries)

    • setValues

      public void setValues(GeoValues values)

    • setWebLinks

      public void setWebLinks(Collection<String> webLinks)